Is BRAP p.Met441Val (c.1321A>G) pathogenic?

BRAP p.Met441Val (c.1321A>G) is classified Uncertain significance in BRAP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-22). AlphaMissense: ambiguous (0.365); Absent from gnomAD v4.1.

How common is BRAP p.Met441Val (c.1321A>G) in the general population?

BRAP p.Met441Val (c.1321A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BRAP p.Met441Val (c.1321A>G)?

AlphaMissense predicts ambiguous (score 0.365) — an in-silico prediction, not a clinical call.

BRAP p.Met441Val

c.1321A>G · VCV3825238

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.365 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.365	ambiguous
REVEL	0.18	moderately benign-leaning
SaProt	LLR -5.26	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 1.7, phastCons 1
Regional constraint	o/e 0.75	unconstrained · MANE · 14 kb · p 0.0006 · regional, not allelic
Overall
CADD	21.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BRAP
Protein: p.Met441Val
Coding: c.1321A>G
MANE Select: NM_006768
Type: single nucleotide variant
Location: chr12:111650033 (GRCh38)
Gene constraint: LOEUF 0.766 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.92

Full BRAP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BRAP p.Met441Ile Uncertain significance ★ ⚠ same residue
BRAP p.Met441Leu Uncertain significance ★ ⚠ same residue
BRAP p.Ala42= Benign ★★ same type
BRAP p.Gly250= Benign ★★ same type
BRAP p.Ile193= Benign ★★ same type
BRAP p.Lys451= Benign ★★ same type
BRAP p.Ala100Val Uncertain significance ★ ⚠ same type
BRAP p.Ala379Val Uncertain significance ★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/brap-p-met441val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown